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- PDB-7p44: Structure of CgGBE in P21212 space group -

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Basic information

Entry
Database: PDB / ID: 7p44
TitleStructure of CgGBE in P21212 space group
Components1,4-alpha-glucan-branching enzyme
KeywordsCARBOHYDRATE / glycogen branching enzyme
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / fungal biofilm matrix / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytosol
Similarity search - Function
1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set ...1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
1,4-alpha-glucan-branching enzyme
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBallut, L. / Conchou, L. / Violot, S. / Galisson, F. / Aghajari, N.
CitationJournal: Glycobiology / Year: 2022
Title: The Candida glabrata glycogen branching enzyme structure reveals unique features of branching enzymes of the Saccharomycetaceae phylum.
Authors: Conchou, L. / Martin, J. / Goncalves, I.R. / Galisson, F. / Violot, S. / Guilliere, F. / Aghajari, N. / Ballut, L.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-alpha-glucan-branching enzyme
B: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,5366
Polymers162,2882
Non-polymers2484
Water7,314406
1
A: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3925
Polymers81,1441
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-alpha-glucan-branching enzyme


Theoretical massNumber of molelcules
Total (without water)81,1441
Polymers81,1441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)210.026, 88.615, 89.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 1,4-alpha-glucan-branching enzyme / Glycogen-branching enzyme


Mass: 81143.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: GLC3, CAGL0M03377g / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express
References: UniProt: Q6FJV0, 1,4-alpha-glucan branching enzyme
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 5.6
Details: 0.1M trisodium citrate pH 5.6, 10% PEG 4000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→46.85 Å / Num. obs: 65906 / % possible obs: 99.4 % / Redundancy: 4.9 % / CC1/2: 0.994 / Rrim(I) all: 0.174 / Net I/σ(I): 6.62
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 1.58 / Num. unique obs: 7507 / CC1/2: 0.777 / Rrim(I) all: 0.854

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZY

4bzy


Resolution: 2.4→46.85 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 3291 5 %
Rwork0.2107 62570 -
obs0.2126 65861 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.59 Å2 / Biso mean: 54.7203 Å2 / Biso min: 20.21 Å2
Refinement stepCycle: final / Resolution: 2.4→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11089 0 16 406 11511
Biso mean--40.44 43.82 -
Num. residues----1387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.430.40731360.36362573100
2.43-2.470.34611340.3337259499
2.47-2.510.421350.31492555100
2.51-2.550.31591350.29262574100
2.55-2.590.32541360.29572586100
2.59-2.640.38031370.28162597100
2.64-2.690.32571370.26722595100
2.69-2.750.29231350.24752572100
2.75-2.810.30521360.2532611100
2.81-2.870.31071370.23972591100
2.87-2.940.27481360.24352585100
2.94-3.020.29591370.25642593100
3.02-3.110.32361350.26052592100
3.11-3.210.29621380.24322626100
3.21-3.330.30251380.23362610100
3.33-3.460.24871370.20922612100
3.46-3.620.27231370.19642603100
3.62-3.810.20861390.18722624100
3.81-4.050.19621380.1764262699
4.05-4.360.18451370.1564259899
4.36-4.80.1488138262999
4.8-5.490.2081390.167264999
5.49-6.920.20171410.1874267698
6.92-100.19721430.1704269995
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08630.0101-0.08670.0383-0.06170.1399-0.01060.0189-0.25970.07140.12370.09470.04440.0586-00.2937-0.0243-0.00460.2920.04760.4603-26.255-12.414-35.978
20.1073-0.01710.06210.0147-0.00330.0204-0.0616-0.21950.060.05240.0259-0.31430.04690.05100.28550.0133-0.00920.3734-0.04570.2946-3.34112.239-27.694
30.07770.03090.09390.09220.0020.1424-0.0407-0.02180.2137-0.0739-0.0752-0.42970.0320.1738-0.00330.2423-0.0118-0.0240.2965-0.05030.54535.58420.858-34.825
40.099-0.1171-0.06480.11420.06090.0242-0.0134-0.12920.08370.0870.0389-0.1490.0432-0.058900.2906-0.01070.01460.3136-0.03760.4006-15.94724.499-33.532
50.3472-0.15040.13720.1299-0.13690.01590.0048-0.0340.1582-0.02120.0208-0.081-0.01090.0265-00.2464-0.00430.01240.2667-0.02060.2644-21.34814.855-39.761
60.1445-0.1045-0.03230.1940.18160.1240.04540.08930.1708-0.1975-0.1420.02980.01950.099600.3279-0.0018-0.01770.28650.00630.4551-42.16311.088-49.331
70.2818-0.1745-0.03860.2730.0127-0.02550.0239-0.03870.1063-0.0543-0.07050.14150.01620.036300.27080.0195-0.0140.2451-0.01010.3836-45.58624.285-46.113
80.14220.0590.04630.04280.09290.23030.04960.02970.0849-0.02010.03160.40360.0015-0.0397-00.26280.01010.01450.25610.00990.6457-64.04415.824-38.351
90.9076-0.0325-0.02860.7463-0.29470.1992-0.01660.11650.1557-0.11210.08210.12070.02870.0518-00.4050.0063-0.06920.41960.02740.3214-20.6539.166-78.796
100.0863-0.03160.02640.1226-0.04790.01960.02210.3166-0.1124-0.2790.06790.02640.15050.0888-0.00030.57940.0133-0.04620.6218-0.14650.2413-13.13920.098-84.713
110.26460.05350.14020.1536-0.03410.0797-0.03330.1052-0.201-0.31240.23120.30360.08460.05210.10360.7992-0.0789-0.3880.5048-0.06310.742-40.0027.942-89.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:43 )A1 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:91 )A44 - 91
3X-RAY DIFFRACTION3( CHAIN A AND RESID 92:146 )A92 - 146
4X-RAY DIFFRACTION4( CHAIN A AND RESID 147:196 )A147 - 196
5X-RAY DIFFRACTION5( CHAIN A AND RESID 197:430 )A197 - 430
6X-RAY DIFFRACTION6( CHAIN A AND RESID 431:502 )A431 - 502
7X-RAY DIFFRACTION7( CHAIN A AND RESID 503:625 )A503 - 625
8X-RAY DIFFRACTION8( CHAIN A AND RESID 626:706 )A626 - 706
9X-RAY DIFFRACTION9( CHAIN B AND RESID 6:359 )B6 - 359
10X-RAY DIFFRACTION10( CHAIN B AND RESID 360:444 )B360 - 444
11X-RAY DIFFRACTION11( CHAIN B AND RESID 445:705 )B445 - 705

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